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Welcome back, Brontosaurus! And other first thoughts on Tschopp et al. (2015)

April 7, 2015

YPM 1980: Brontosaurus excelsus, the animal formerly known as Apatosaurus excelsus, the animal formerly known as Brontosaurus excelsus.

Today is a good day for sauropod science. Since we’re not getting this up until the afternoon, you’ve probably already seen that Emanuel Tschopp and colleagues have published a monstrous specimen-level phylogenetic analysis of Diplodocidae and, among other things, resurrected Brontosaurus as a valid genus. The paper is in PeerJ so you can read it for free (here).

I’ve already been pinged by lots of folks asking for my thoughts on this. I know that the return of Brontosaurus is what’s going to catapult this paper into the spotlight, but I hope what everyone takes away from it is just what a thorough piece of work it is. I’ve never seen so many phylogenetic characters illustrated so well. It sets a new standard, and anyone who wants to overturn this had better roll up their sleeves and bring a boatload of data. I’m also very, very happy that it’s open-access so everyone in the world can see it, use it, question it, tear it apart or build on it. Getting Brontosaurus back is just gravy. Although, being pro-brontosaur enough to have named a dinosaur in honor of Brontosaurus, I’m also pretty happy about that. If you need a quick guide to who’s who now, A. ajax and A. louisae are still Apatosaurus, and B. excelsus, B. yahnahpin (formerly Eobrontosaurus), and B. parvus (originally Elosaurus) are all Brontosaurus. For more details, go read the paper.

Apatosaurus lousiae CM 3018: still Apatosaurus. Photo from Wikipedia.

My personal feelings aside, a lot of people are asking how solid is this generic re-separation. I haven’t read the entire paper yet – it’s 299 pages long, for crying out loud – but the separation of Brontosaurus and Apatosaurus seems solid enough. Tschopp et al. didn’t do it lightly, they justify their decision in detail. I don’t hold with the idea that just because two taxa are sisters, means that they cannot be separated generically. As usual in phylogenetic taxonomy, it comes down to what we decide as a community constitutes “diagnosably distinct”. Tschopp et al. have actually put some thought into what that might mean here, and whether you agree with them or not, they’ve at least made all of their evidence and reasoning explicit. That’s both an opportunity and a challenge for critics: an opportunity to pin down exactly where and why you may disagree, and a challenge to do exactly that. You can’t just sit back and say, “I think the analysis is flawed” or “I wouldn’t have coded that character that way” (well, you can, but if that’s all you say, no-one is obliged to take that kind of lazy, drive-by criticism seriously). There are 477 characters here, most of them illustrated, for 81 OTUs, and a lot of post-hoc discussion of the results. So whether you agree with the authors or not, in whole or in part, both fans and critics should dig in and build on this work. Is it the last word on diplodocid taxonomy? Of course not. But it does move the field forward significantly, and the Tschopp et al. should be applauded for that.

There’s a lot more in there than just bringing back Brontosaurus. “Diplodocus” hayi is elevated to its own genus, Galeamopus. Neither of those things are super surprising. There have been rumors since the 90s at least that Brontosaurus might be coming back, and everyone has known for a while that D. hayi was a bit wonky. I was also not surprised to see Australodocus returned to Diplodocidae – when I saw the type material in 2011, it looked diplodocid to me (based on some characters I’ll have to unpack in some other post). More surprising to me are the sinking of Dinheirosaurus into Supersaurus, the finding that Tornieria is not particularly close to Diplodocus, and the uncertain positions of AMNH 460, the American Museum mount, which is an indeterminate apatosaurine pending further study, of FMNH 25112, the Field Museum “Apatosaurus”, which might not even be an apatosaurine at all(!). In several cases, Tschopp et al. come right out and say that X is going to need further study, so if you want to work on sauropods and you’re stuck for project ideas, go see what needs doing.

AMNH 460: we don’t know who this is anymore.

As I was scanning the paper again while composing the last paragraph, I almost fell down the rabbit hole. So much interesting stuff in this paper. Even if all you care about is morphology, the hundred or so figures illustrating the phylogenetic characters ought to keep you happy for a very long time. I look forward to reading through the vertebral characters in detail and seeing what I’ve been missing all these years.

I’m contractually obliged to point out that the authors chose to publish the complete peer-review history of the paper, so you can see what the editor (Andy Farke) and reviewers had to say. As always, I think this transparency (and credit for the reviewers) is great for science, and I can’t wait until it’s the norm at more journals.

FMNH 25112: what even IS that thing?

In addition to the paper, there’s also an interview with lead author Emanuel Tschopp on the PeerJ blog, and a nice shout-out for SV-POW!

Parting shot: why did Tschopp et al. get different results than anyone had previously? Because they used more specimens and more taxa – more data full stop. That’s also why their paper warrants serious consideration. It’s serious work. Let’s go stand on their shoulders.

76 Responses to “Welcome back, Brontosaurus! And other first thoughts on Tschopp et al. (2015)”

I heard about this at around 2:00 PM: “Chase, Brontosaurus is back!” and I immediately went online. When I saw the paper I fanboy-ed! Tschopp et. al. did an amazing job with the paper! Their phylogenic analyses were rigorous and they supported their theories with accurate data. The vigorousness of the paper is unlike anything I have seen on diplodocoidea yet. I cannot praise them enough for their work (which took 5 years, gosh darn it!), and I congratulate them on being the authors of one of the most rigorous studies on any group within Dinosauria ever. Nice work, guys.

OK, I’ll wade in as a dissenter (somewhat, not 100%). Yes, I agree this is an impressive piece of work worthy of emulating. What concerns me (somewhat) is that practically all sauropod specimens became separate taxa. There is a lack of generic or
species unity partially because no one has really figured out how to incorporate ontogenetic scoring changes. McIntosh attempted to do that using his brain-powered computer (which I think is sometimes underrated). But many now tend to dismiss such a “primitive” method as somehow “less scientific” because no computer was used. The result is that sometimes people don’t step back and ask themselves: “do these results make sense?” In other words, there is a lack of a reality check. Consequently, I have seen (and I am sure others have) some really dumb conclusions. I won’t mention examples so as not to publicly embarrass the guilty, who do not work on saurischians. A reality check would have made the guilty look closer at where they went wrong before publication.

The closest to figuring out ontogenetic scoring is Prieto-Marquez’s dissertation “PHYLOGENY AND HISTORICAL BIOGEOGRAPHY OF HADROSAURID DINOSAURS”. Oddly, Prieto-Marquez has not published some of the important parts of his work. Does he doubt himself? Did he get so much negative responses in review that he pulled it? I suspect that to really make a break through in ontogentic scoring is going to require fuzzy computing, something our simple binary computers are not yet capable of very well. Oddly, the human brain is quite capable of fuzzy computing, but that is not very “scientific” to some people (someone want to tell Steven Hawking that? or Charlie Darwin?) .

There is also the not-so minor problem that most of the mounted specimens used in this and other studies have been heavily restored with liberal amounts of plaster and paint. Even specimens in older collections are not fully trustworthy because of the same reason. This can and does impact scoring.

I agree. I also feel that they could have factored in phenotypic variation more. Specimens which Tschopp et. al. defined as distinct taxa based on features which they have defined as autapomorphies could just be characteristics of that specific animal. The presence of these features may have nothing to do with the animal being in a certain growth stage (even though that is a good hypothesis), but just may be examples phenotypic (and ultimately genotypic) variation.

Now that was a paper worth waiting for.
So we have the restoration of some old names and a new genus.
It looks like when some of the currently unidentifiable skeletons are restudied we will have some more species/genera too.
Nice to see that the LACM Apatosaurus was included when it was left out of the previous Apatosaurus study; however there seems less of it available than when it was originally collected.
I wonder where the rest of it was lost.
It would be nice to see the ?Diplodocus specimens from Poison Creek at the CMM included in a study too; the skeleton and skulls appear fairly complete.
There seems to be considerable variety in the SMA specimens, suggesting some diversity of diplodocines in the area.
Interesting.

As someone who advocated this type of analysis before (I believe Dave and I spoke with Matt about the idea years ago) I stand in awe at how much better this study is than our initial ideas were. That’s not to say there aren’t areas that could be improved (science, duh!), but seriously, this is a fantastic step forward and hopefully a sign of things to come for other groups.

Aaaarrrgh!!! I knew something like this would happen after Matt and I finalized our text for the Johns Hopkins book! In our preface at least we predicted changes like this would occur, all for the good…… Bully for Brontosaurus.

Well, Ken, your reservations are well founded — as always, phylogenetic signal is confounded by ontogeny and by ill-advised “restoration” of specimens (and indeed individual variation, as Chase noted). I suppose my question would be: do you feel that the Tschopp et al. paper is any more affected by these issues than anyone else’s?

One of the ways in which Tschopp et al. have made their work particularly objective is in their attempt to establish numeric criteria for generic and species-level distinctiveness. That makes their conclusions simultaneously more vulnerable to specific, grounded criticism, and pretty much immune from “Yeah, I just don’t by it” drive-bys. I admit I’ve yet to closely read the parts of the paper that explain this, so it’ll be interesting to see what I make of it — and what others have to say.

“Oddly, the human brain is quite capable of fuzzy computing, but that is not very “scientific” to some people (someone want to tell Steven Hawking that? or Charlie Darwin?).”

That’s a bit of a red herring. Hawking and Darwin made their name on conceptual breakthroughs, which are all about mental flexibility, innovation and creativity — areas where computers are always going to be weak. What we’re talking about is crunching numbers, and area where they surpass even the greatest human brains by orders of magnitude.

This new paper is very cool for the huge phylogenetic work done. Congrats to Emanuel and his co-authors.
On the (abused) taxonomic side of the paper. Until someone explicitly defines Apatosaurus as “everything closer to A. ajax than B. excelsus” and Brontosaurus as “everything closer to B. excelsus than A. ajax”, the question of what is Brontosaurus/Apatosaurus remains totally subjective, regardless to the metric used to “quantify” a genus. This just because taxa-name are taxo-nomic issues, not systematic (phylogeny-ontogeny-stratigraphy problems).

Well Mike, I too was given the pre-publication Tschopp et al. by the Scientific American writer Choi (I saw your name among those initially contacted), so my comments are not drive by pot shots. I should have also added phenotypic variation is not utilized well under the current binary software, but Chase covered that for me. This form of variation was covered by Prieto-Marquez’s dissertation.

Various methods have been proposed by others to deal with this problem by using an average of a phenotypic character or ignoring extremes, but that is cheating because that denies the existence of variability, so from the beginning is biased. I pointed that out when I did that paper on the skull bones of Allosaurus from the Cleveland Lloyd Dinosaur Quarry. There were two short maxilla from two individuals that were not juveniles, so ontogeny was not a factor in the shortness. Standard procedure has been to ignore them as “abnormal” (“they look different, so they must be pathologic and can be ignored”). But aside from abnormal shortness, they are indistinguishable from other specimens from the same quarry, same layer, and most-likely from the same population. The typical method of dealing with these using phylogenetic software is to ignore them as extremes or to say they cluster differently, so must be a different taxon. Variation is not an option, which is not the real world.

And no, Hawking and Darwin are not red herrings. The published mistakes I referred to would not have appeared had the authors gone beyond accepting the number crunching results at face value, but instead asked “is this result reasonable?” To question one’s results does not seem to have occurred to them. I can’t see where Tschopp et al. questioned their own results that almost all of the Morrison diplodocids seem to be separate taxon. That is what I question. I ask you, Mike, using your accumulated of data from looking at specimens up close and personal now stored in your brain, does that seem reasonable?

Until we develop computers and software that accept that a character can be both 0 and 1 at the same time (fuzzy computing), then we will never acknowledge variation and not have a true picture of phylogeny. None of what I write is new; others have pointed out problems with scoring. I have seen non-saurischian papers in which the author acknowledged both phenotypic conditions were present in the sample studied, but decided to score the character as 1 for analysis. Doing so has already biased the results.

Now comes the big BUT, which is why I don’t totally think Tschopp et al are wrong: the specimens come from different stratigraphic levels in the Morrison and from different geographical areas. Thus, the majority of the specimens do not come from the same population (i.e., group of breeding individuals). On that basis, it may very well be that the diversity of diplodocid species through time and geographic distribution may very well be represented in the specimens used. Unfortunately, we still cannot place the majority of the specimens within the 10 million years represented by the Morrison. So I cannot rule out that the specimens really do represent different taxon as Tschopp et al think. In the end, I think phylogenetic analysis today at most gives us a peak of what MIGHT be, rather than what IS, so we might as well chill and take the results not so seriously.

Technically the paper is a couple orders of magnitude past nearly all other phylogenetic analyses of Mesozoic dinosaurs. Detailed character descriptions (as in Rauhut, 2003), extremely transparent procedures, explicit discussion of resulting trees with lengths and supporting characters, etc.. No idea how accurate the codings are since this isn’t my forte, but they examined basically all specimens firsthand.

One issue I have is that because the Diplodocus longus holotype was found to be indeterminate within Diplodocus, Tschopp et al. are “suggesting the suppression of D. longus as type species of Diplodocus, and its replacement by D. carnegii.” I swear that Wilson and Upchurch’s Titanosaurus paper has harmed more in dinosaur taxonomy than any other. I will repeat for the nth time- NOTHING in the ICZN states the type species of a genus or the type genus of a family level taxon needs to be diagnostic. It needs to be nomenclaturaly valid as both Titanosaurus and D. longus are, but not taxonomically diagnostic. Note that contra Tschopp et al., this is not like the case of Cetiosaurus medius vs. oxoniensis. In that case, who knows what medius is. There’s no reason to think it’s closer to oxoniensis than to any other eusauropod, but longus is agreed here to be closer to carnegeii and hallorum than lentus, etc..

There’s also some nonsensical taxonomic/nomenclatural discussion. laticollis is 1. “considered a nomen dubium”, 2. “referred to A. louisae” and 3. acknowledged to “have priority over A. louisae.” You can’t have those all at once! If it’s the same species as louisae, it’s the proper name for that species. If it’s a nomen dubium, it cannot be referred to louisae.

Besides this, the authors have created a genericometer of sorts, but without showing their distance or character difference methods are valid for other agreed upon scenarios (e.g. modern species; T. rex), they don’t accomplish much. Their cladogram is perfectly congruent with Apatosaurus excelsus or Barosaurus siberi. I suspect if we applied their methods to other areas of Dinosauria, we’d get results at least as different as Paul’s field guide. So it’s not like Tschopp et al. discovered Brontosaurus was valid, they merely used methods no other Mesozoic dinosaur researcher has used to propose its validity.

Well Mike, I too was given the pre-publication Tschopp et al. by the Scientific American writer Choi (I saw your name among those initially contacted), so my comments are not drive by pot shots.

Oh! In case it wasn’t clear, I didn’t at all mean you when I wrote that — I wouldn’t remotely characterise your comments as drive-bys.

Various methods have been proposed by others to deal with this problem by using an average of a phenotypic character or ignoring extremes, but that is cheating because that denies the existence of variability, so from the beginning is biased.

I wouldn’t call it cheating. All science is based to some degree of finding acceptable simplifications. At GCSE, physicists neglect friction. At A-level, they start taking friction into account, but still neglect air-resistance. Nearly all the work of even professional engineers uses Newton’s approximations to Einsteinian mechanics on the basis that the relativistic effects are too small to be worth bothering with. That’s appropriate: in the trade-off that buys more accuracy in exchange for more effort, you have to make a judgement when the additional accuracy is just not worth the work. Arguably, the ability to do that — to “concentrate on the high-order bits”, as Scott Aaronson puts it, is one of the qualities that makes a good scientist.

So: already our sequences of character-scores are no more than crude proxies for the specimens that they represent. I don’t think anything about that changes fundamentally when we average variable characters, or code their range, or whatever other solution we come up with.

I pointed that out when I did that paper on the skull bones of Allosaurus from the Cleveland Lloyd Dinosaur Quarry. There were two short maxilla from two individuals that were not juveniles, so ontogeny was not a factor in the shortness. Standard procedure has been to ignore them as “abnormal” (“they look different, so they must be pathologic and can be ignored”). But aside from abnormal shortness, they are indistinguishable from other specimens from the same quarry, same layer, and most-likely from the same population. The typical method of dealing with these using phylogenetic software is to ignore them as extremes or to say they cluster differently, so must be a different taxon. Variation is not an option, which is not the real world.

This is a nice example of why we need palaeontologists to do palaeontology, and can’t hand it all over to computers. The fundamental problem with computer programs is that they are only capable of formulating hypotheses of the kind they have been programmed to. Great at saying “the most parsimonious phylogenetic hypothesis to account for this character matrix is that tree”; terrible at saying “hey, that gives me an idea!”

And no, Hawking and Darwin are not red herrings. The published mistakes I referred to would not have appeared had the authors gone beyond accepting the number crunching results at face value, but instead asked “is this result reasonable?” To question one’s results does not seem to have occurred to them.

I suppose I can neither agree or disagree without knowing which papers you’re alluding to. My point, which may not be in opposition to yours, is that the kind of cogitation Darwin did is a fundamentally different of activity from what computers are doing when they figure out most-parsimonious trees.

I can’t see where Tschopp et al. questioned their own results that almost all of the Morrison diplodocids seem to be separate taxon. That is what I question.

Well, first of all, what they mostly found was that many of the type specimens belong to different species — which shouldn’t be hugely surprising. That is mostly a validation of older, pre-cladistic work, not an overturning.

The second thing to note is that this was by no means the only kind of conclusion they came up with. Notably, they found Dinheirosaurus to be yet another synonym of Supersaurus (along with Dystylosaurus, Ultrasaurus and Ultrasauros). Ironically, this of all their conclusions is the one that I do feel intuitively inclined to be sceptical about — congenericity of sauropod species from different continents does not have a good track record, as “Barosaurus” africanus and “Brachiosaurus” altithorax will testify.

Thirdly, Tschopp et al. are pretty clear about their measures of whether two specimens should be considered to belong to the same species or genus, and they lay our reproducible ways for people to run those same routines. That’s commendable.

And the fourth thing is that in calibrating the genericometer, the only sensible thing to do is use similar distances to those that pertain elsewhere in the same clade — which again is what Tschopp et al. did. It’s no use saying “But Quercus has 800 species, so all sauropods should be lumped into Cetiosaurus” — it’s just not how things are done in sauropod studies.

So what it comes down to is this: on what basis should Tschopp et al. have lumped more aggressively than they did? And the only possible answer seems to be: because you prefer larger genera with more species. Which is at best a personal preference, and at worst at odds with how the rest of the sauropod tree is interpreted.

(As an aside: for large animals whose remains tend to be incomplete and which for that reason are often not very stable within the phylogenetic tree — in other words, for sauropods — I favour monospecific genera for the practical reasons that the resulting names don’t need to be changed when the tree reshuffles.)

I ask you, Mike, using your accumulated of data from looking at specimens up close and personal now stored in your brain, does that seem reasonable?

To me, it does. But I accept that others might disagree.

Until we develop computers and software that accept that a character can be both 0 and 1 at the same time (fuzzy computing), then we will never acknowledge variation and not have a true picture of phylogeny.

Wait, that’s no trick. Even PAUP* handles multi-state scores. We’ve been doing this for two decades.

None of what I write is new; others have pointed out problems with scoring. I have seen non-saurischian papers in which the author acknowledged both phenotypic conditions were present in the sample studied, but decided to score the character as 1 for analysis. Doing so has already biased the results.

Again, I can’t comment on the specific because I don’t know what it is is. But I could imagine looking at, say, a population of nice, complete Protoceratops, seeing that all but one of them have the same score for a character, concluding that the one is an aberration, and scoring the majority. Is that what happened? If so, I can’t see at the moment what the problem is with that.

Now comes the big BUT, which is why I don’t totally think Tschopp et al are wrong: the specimens come from different stratigraphic levels in the Morrison and from different geographical areas. Thus, the majority of the specimens do not come from the same population (i.e., group of breeding individuals).

In the end, I think phylogenetic analysis today at most gives us a peak of what MIGHT be, rather than what IS, so we might as well chill and take the results not so seriously.

No argument there!

In the end, one of the best reasons for running your own phylogenetic analysis (even if, as in my case, it’s only by piggy-backing new taxa onto others’ existing matrices) is that it gives you healthy degree of scepticism about the outputs of all phylogenetic analyses.

Well, Mickey, their cladogram is also perfectly congruent with Diplodocus excelsus and Diplodocus siberi. You don’t need me to tell you that you can’t do taxonomy just by looking at a tree, however well supported.

Regarding the switch in type species of Diplodocus: you are quite right that ICZN rules don’t mandate a change due to the non-diagnostic nature of the present type material — any more than they mandated a switch away from Cetiosaurus medius. That is precisely why a petition is needed, rather than a simple statement in the paper. The simple truth is that whenever anyone says “Diplodocus”, what they mean by that term is “CM 82 and sufficiently closely related individuals”. A petition to bring the official nomenclature in line with that reality is welcome. I, for one, will be following Tschopp et al. in using D. carnegii as though it were the type species — since in practice it has been ever since 1901.

Hi Mike,
First, to correct a typo, “peak” should be “peek”. Then tweak the multistate character comment, which should refer to my first comment, meaning that we cannot score for the ontogenetic change in a character because there is a point when a character is a “shade of grey”.

There is another problem with current phylogenetic methodologies, namely that it is reductionist as you point out. But in the real world, including quantum physics, the whole is greater than the sum of the parts. This is the property of emergence. I haven’t seen anyone apply emergence to phylogenetic analysis. Is it even possible?

As for longus, it is of course in that as yet unpublished manuscript of mine. It was originally a Carpenter, Tidwell and McIntosh production, then a Carpenter and Tidwell production and has been a Carpenter production for the past 5 years. Part of the separation of McIntosh and Tidwell was over hayi. Neither wanted to move it to its own genus and Tidwell was leery of the phylogenetic result of the diplodocids (but I also suspect she dropped out because she was and is pissed at me leaving Denver). As I once told you, nag me about the manuscript on occasion – it repeatedly keeps getting moved forwards and backwards in levels of priority. I can say, however, that longus can be diagnosed.

By the way, I have grown accustomed to the avatar that was assigned to me. It reminds me of the comment made by Russell Crowe as Captain Aubrey in Master and Commander to the proto-Darwin character, Dr. Maturin: “name something prickly after me.”

I have to say, this is the best news I have heard about concerning new sauropod research. Although I would love Brontosaurus to be a valid genus again. Tschopp etl .have added as mentioned a lot to sauropod phylogenetics.
However, after reading the posts, and seeing the various specimens on display. I may have to agree with Carpenter’s points with all specimens becoming too many separate taxa. How do we know what is ontogeny and variation within the species itself? It remind me of the whole Tyrannosaurus and Tarbosaurus, and the Brachiosaurus/Giraffititian deal.. I also have to agree with Horner’s statement,”too many species have been named”. I think this applies to many dinosaur species and families in general. Greg Paul has an idea that is controversial as far his classifications go with many paleontologist. However, he does bring up some good points.
Best analog that comes to mind is the relationship between the American Alligator and the Chinese Alligator. There are variations between these two species having to due with size and number of teeth. Along with some minor cranial differences between the two, but yet they are still alligators. Unlike their differences with species of Crocodylus.
Another example are African and Asian elephants, again there are some minor morphological differences. Asians have two small humps on the head, the African does not. They are still elephants, differences are not as great say with Loxodonta compared with Mammuthus.
I feel the tyrannosaur/tarbosaur situation is analogous to the alligator relationships. While the American and African Brachiosaurid species fit the African and Asian elephant scenario.
So should the diplodocid relationships be more like the alligators? Or is it more like the Loxodonta and Elephas model? Only more research and specimens will tell. Till then Tchopp etl. has made a great contribution that gives all of us sauropod lovers food for thought!

Thank you all for the discussion, which really helps with understanding the paper. I can only add that I am definitely looking forward to explaining “indeterminate apatosaurine” to Saurischian Hall visitors!
– Jerry Alpern
Volunteer Tour Guide, AMNH

While I have to say that, as I get older, I tend to trend toward lumping, I’m also going to say that assessing ontogeny was not necessarily within the scope of this paper. I think it’s a very valuable paper and if a bunch of species are named, that’s ultimately a Good Thing. Only after this sort of sorting is done can people start to dig a little deeper, but the groundwork has to get done first. This is the groundwork.

One area of research I’d like to see follow-up on is taking old, well-known mounts and figuring out what is and isn’t restored. Andy Farke did that for Nedoceratops and I think it would be very valuable for some of these sauropod specimens.

Zach, I think everyone would love to know what is and isn’t restored in old mounts! A few years ago I went to the Yale Peabody Museum specifically in order to personally inspect the neck of Apato^H^H^H^H^HBrontosaurus. The YPM staff were super helpful and provided me with stepladders, lighting, etc. Still, I could make out almost nothing. I came away without a much clearer idea than I’d already had of how much of the cervical material is real. The only solution is to dismount the material, re-prepare it, study it and re-mount it. In fact, YPM are keen to do this, but you can imagine how expensive and disruptive such a project would be.

Matt: you may “agree with Horner’s statement, ‘too many species have been named'”, but unless you have something more concrete to say in its defence, you’re not doing more than expressing a personal preference, much along the lines of “Pralines and Cream tastes better than Phish Food”.

In the case of Brontosaurus, we’ve had a subjective taxonomic consensus that would still work for Tschopp et al.’s tree. The only reason for raising excelsus to genus level is that the authors use new methods not previously employed for Mesozoic dinosaurs. I don’t mind if the new subjective consensus is to recognize Brontosaurus, but it’s not due to any objective new information, just that this is the most detailed study of Mesozoic dinosaur phylogeny, so is going to be followed.

In the case of Diplodocus, the situation is different than for Cetiosaurus. Cetiosaurus needed it more because medius has no clear relation to oxoniensis past Eusauropoda. Thus the alternative was to keep Cetiosaurus medius as some poorly known eusauropod with no established diagnosis and create a new genus for oxoniensis that would replace what we’ve thought of as Cetiosaurus for decades. Yet longus is already supported as closer to carnegeii and hallorum than any other named genus. So why not just have diagnostic Diplodocus containing diagnostic carnegeii and hallorum and undiagnostic longus? Why is that so problematic that we need an ICZN ruling?

Further, Carpenter doesn’t think longus is indeterminate, and just because there are no autapomorphies in a phylogenetic analysis doesn’t mean a taxon is undiagnostic. Does it have a unique combination of included characters? Does it differ in characters that weren’t included? We don’t know. Why are people so eager to sink taxa (Allosaurus fragilis holotype, Stegosaurus armatus holotype, etc.) before the basic work has even been done or a consensus been developed?! Surely before we resort to getting the ICZN to change the rules, we should do the science to demonstrate they need changing and get a consensus.

“So why not just have diagnostic Diplodocus containing diagnostic carnegeii and hallorum and undiagnostic longus? Why is that so problematic that we need an ICZN ruling?”

Because it doesn’t reflect the reality of what people actually mean when they use the name “Diplodocus“. I am more interested in having our nomenclature reflect reality than I am in having it adhere to an ultimately arbitrary set of rules — and so is the ICZN.

Sure, but that’s an accident. When people say “Diplodocus” they mean D. carnegii. You can tell that this is true by the following thought experiment. Suppose D. longus turned out to be closer to Barosaurus than to D. carnegii: would people’s conception of Diplodocus change? No. It’s anchored on carnegii. It may not be what the ICZN’s legal code says should happen, but it’s the state of the world as we actually find it.

Hmm, if most people mean carnegii when they say Diplodocus, why include hallorum? Most people, when discussing hallorum, still qualify it with (Formerly Seismosaurus). Just using Seismosaurus again would reduce word count, at least ;)

I agree with Mike that we should just use monotypic genera, rather than constantly reshuffling names. This would even work if some lineages turn out to be anagenic. After all, aren’t Eobrontosaurus, Elosaurus, Brontosaurus, A. louisae, Apatosaurus, and Amphicoelias roughly segregated from each other from low to high in the Morrison in that order?

Until we develop computers and software that accept that a character can be both 0 and 1 at the same time (fuzzy computing), then we will never acknowledge variation and not have a true picture of phylogeny.

As mentioned above, it has “always” been possible to score a taxon in a computerized data matrix as having states 0 and 1 of any character (or indeed 0, 1 and 2, and so on). I’m pretty sure Hennig86, from 1986, already let you do that. That’s what phylogeny papers mean by “polymorphism” and “polymorphic”.

John J. Wiens and varying coauthors have even developed approaches that let you take into account how common each state is in the large representative population of extant herptiles one is studying. :-) I work on animals that are on average as uncommon as sauropods, so I haven’t actually looked into such methods, but they exist (or at least one does).

For ontogeny, I prefer a slight modification of an approach developed in this paper (where Wiens is, perhaps unsurprisingly, the first author; access is now open): if there’s a taxon that is only known from immature or paedomorphic individuals, and the ontogeny of a reasonably close relative is more completely known, then score the first taxon as unknown for those characters where it looks potentially immature compared to its relative. I’ve discussed this at some length in this paper (which is in open access, except that the publisher’s website has been “under construction” for well over a year now, so I feel free to tell the public to contact me). Often this involves partial uncertainty for multistate characters: if babies of the better-known relative have state 0 and full-grown adults have state 5, while the only known individual of the taxon you’re trying to score shows state 3, then score it as having state 3, 4 or 5, but not 0, 1 or 2. In available software it has been possible to score partial uncertainty for as long as polymorphism.

Of course this approach to dealing with ontogeny is not fully objective; “reasonably close relative” cannot be reasonably defined, for example. :-) But so far it seems to be working pretty well; I’ll soon submit the next manuscript that uses it.

It should be mentioned — and indeed, will be, now — that there’s more than one output phylogeny from Tschopp et al. (2015). Specifically, there are various a posteriori deletions of specimens, as well as a priori analyses running “pruned” of these specimens, and they results in a variety of other topologies for specimens included. While this work is exemplary, it is not in a bubble to itself. The authors chose to support the strict consensus for purposes of taxonomy; whereas the pruned tree results in a radical topology that, had it been employed to their metric, would yield differing results. We’d likely be looking at even more diverse taxonomy. So a subjective choice in tree results in subjective metric of character “changes” along the branches, which resulted from itself selected characters chosen, an absence of clear ontogenetic assessment (work by Fowler and others deems ontogeny important and relevant to diplodocoids!), and thus, arriving at … Brontosaurus!

As an added point, to the initial post, the comments about how Brontosaurus might be separated are based on Robert Bakker’s touting of a study, never done, that supported diverse cranial morphology between Apatosaurus and Brontosaurus. Not ajax and excelsus, mind you; but the genera, as if this could be determined.

Taxonomy will always be subjective. There is no way to perform it with objectivity, save rules governing other aspects relating to it (such as classification). Applying a subjective split to subjective methods in order to obtain some objectivity will always bear fruit for the moment.

In the next instance, Brontosaurus will vanish. In the next after that, all “genera” ever coined amongst sauropods will become valid. Raising one system above the others only tends to reveal the bias of the individual, for either the splitting of taxa, or their lumping.

“Suppose D. longus turned out to be closer to Barosaurus than to D. carnegii: would people’s conception of Diplodocus change? No. It’s anchored on carnegii. It may not be what the ICZN’s legal code says should happen, but it’s the state of the world as we actually find it.”

By that logic, you should have petitioned the ICZN to make brancai the type species of Brachiosaurus, because most people’s conception of the genus is based on it. But you chose the better course of action and now peoples’ conception of Brachiosaurus has changed to only be of the less complete altithorax, just as it would change for Diplodocus to only be the less complete longus in your scenario. Note it happens _all the time_ that people’s conception of a taxon is based on a more complete non-type. Just in Sauropoda, Mamenchisaurus hochuanensis instead of M. constructus, Omeisaurus tianfuensis instead of O. junghsiensis, Limaysaurus or Nigersaurus instead of Rebacchisaurus for Rebbachisauridae, Apatosaurus louisae CM 3018 instead of A. ajax’s type, etc.. In Theropoda, the types of such famous genera as Microraptor (back half of skeleton with no leg remiges), Confuciusornis (skull), Velociraptor (skull plus claw), Deinonychus (foot), Tyrannosaurus (partial skeleton with four external skull bones), Albertosaurus (partial skull), Tarbosaurus (skull and some vertebrae), Ornithomimus (partial foot and metacarpus) and Therizinosaurus (claws and ribs) are all based relative crap compared to the specimens people think of when they hear the name or mostly code from. But none have ever been considered for ICZN petitioning, which is good.

But none of this should matter because there’s no reason to think longus will become separated from carnegeii. You don’t petition the ICZN because a situation _could_ occur in the future, and indeed that’s not why Tschopp et al. are petitioning. They are doing so because of “the taxonomically unsatisfying situation that the otherwise well-known genus Diplodocus is typified by a dubious species.” But if Titanosauria/iformes and Ceratopsia/idae are fine, Diplodocus/idae/oidea/etc. should be too.

By that logic, you should have petitioned the ICZN to make brancai the type species of Brachiosaurus, because most people’s conception of the genus is based on it.

I admit a case could have been made for that course of action. But I assume you, and most everyone, would agree with me that in that case it would have been unhelpful. Enough legitimate Brachiosaurus material has been described, and for that matter publicly exhibited, for the type species to have had its own well-defined existence in the minds of both scientists and (segments of) the public.

There are matters of degree. As always in taxonomy, judgement is required. I’m reminded of these observation from Bjarne Stroustrup, the inventor of the C++ programming language:

“There are no ‘cookbook’ methods that can replace intelligence, experience and good taste in design and programming.”

“Design and programming are human activities; forget that and all is lost.”

I’m mainly wondering why Apatosaurus louisae is still Apatosaurus. The major opinions I’ve heard were either that it was a weird specimen significantly different from both ajax and excelsus (and would thus have gained its own genus) or that it was closer to excelsus than to ajax (and would have been transferred to Brontosaurus). I would have favored the latter as ajax appears to be an unusually gracile, long-necked creature compared to excelsus and louisae which are more robust. Actually, the NSMT specimen of ajax looks remarkably like the Field Museum’s specimen; maybe they’re the same taxon.

I’ll have to revise my previous comment. My image of Apatosaurus ajax was based on the widely illustrated NSMT specimen, which according to the analysis is pretty far removed from the main Apatosaurus cluster (and I suspect the referral to ajax was based on the mix-up of the ajax holotype with “Atlantosaurus” immanis, as the later is recovered as sister to the NSMT specimen). The reduced-consensus trees do seem to support to the “louisae is the outlier” view though, with the “execlsus is different” view only supported prior to excluding incomplete specimens, and it strikes me as a bit odd that the former isn’t given more discussion in the paper.

Also, I’m puzzled as to why the authors didn’t include the holotype of Atlantosaurus montanus in their analysis.

I’m afraid that the “Brontosaurus is back!” fanfare is going to increase confusion among the general public though, especially considering the misconception that Apatosaurus was a “replacement name” for Brontosaurus. There will be people wondering why the skulls weren’t changed back, why the skeleton in Pittsburgh is still being called Apatosaurus after the name was changed, and such.

I note you never do engage with my arguments. You can claim taxonomy is as nuanced as you want, but you don’t explain why we need carnegeii as a type species but not constructus or tianfuensis, or why YPM 1920 should not be a holotype but why YPM 5205 and IVPP V10918 are. Or why we should petition the ICZN based on this one study which accessed diagnosticity based on its character list, as opposed to at least waiting for other studies to agree.

The facts are-
– The ICZN doesn’t say anything about needing diagnostic types for any level.
– Numerous taxa are represented by non-type specimens which are more complete and/or used more for coding than their types.
Just what are the negative effects of retaining longus as the type species? You can’t say ‘what if carnegeii is closer to lentus?’ because that has no plausibility of being true.

I note you never do engage with my arguments. You can claim taxonomy is as nuanced as you want, but you don’t explain why we need carnegeii as a type species but not constructus or tianfuensis.

I told you why: that’s the judgement of the people working on those taxa. Not only is there no hard and fast rule, there cannot be any hard and fast rule. The dream of eliminating human judgement from taxonomy is pure fantasy.

Another thought: With ajax represented by one specimen only that came out as basal to louisae, could they be the same species? To do a variation on Riggs’s old argument, perhaps louisae is the adult stage of ajax, as the latter’s type is known to be a subadult.

If you look online there is a copy of Turner and Peterson’s 1999 chapter in the book Vertebrate Paleontology in Utah issue 1.
The chapter is about the biostratigraphy of Morrison dinosaurs and it shows the stratigraphic relationship of the Morrison dinosaur localities in a chart.
If you use the specimens in Tschopp’s paper and look up their locations on the chart the biostratigraphy works quite well, suggesting that there are widespread but short lived rapidly evolving diplodocid species in the Morrison.

Species such as D. hallorum which are known from multiple locations plot in a narrow stratigraphic range; and all the Galeamopus species are older than all the Diplodocus specimens.
The probable new species comprising YPM 1840 and NSMT-PV 20375 is higher up in the stratigraphic column than any other Brontosaurus or Apatosaurus specimen except A. ajax; and Barosaurus comprises B. lentus high up in the stratigraphic column and B. species low in the column at the Howe quarry.

The only discrepancy seems to be the probable new species comprising SMA 0087 from the Howe quarry low in the stratigraphic column and WDC-F S 001A from high up in the column at the BS quarry at the Wyoming Dinosaur Centre.

Also the Dana quarry and Poison Creek specimens which are not covered in Tschopp’s paper are from low in the column and are coeval with the Galeamopus species.

Anyhow, I had been giving some thought to stratigraphy and how it might apply to some of the unknown specimens.

If I remember correctly, the uncertain FMNH specimen was from around the middle of the formation (not very helpful), and the indeterminate AMNH 460 was found near Bone Cabin Quarry, one of the lower sites. That would suggest the latter is Brontosaurus if the stratigraphic separation holds up.

Yes the FMNH P 25112 specimen is from Riggs Quarry 15 which is similar to the Dry Mesa Quarry level; and the AMNH 460 specimen is from the Nine Mile Quarry locality which is below the Bone Cabin Quarry locality and thus slightly lower than the B. yahnahpin locality at Como Bluffs Bertha Quarry.

“I told you why: that’s the judgement of the people working on those taxa. Not only is there no hard and fast rule, there cannot be any hard and fast rule. The dream of eliminating human judgement from taxonomy is pure fantasy.”

Don’t you see that that’s irresponsible and lazy? Just because there will always be some subjectivity involved doesn’t mean you should say ‘just go with whatever the latest workers on that taxon want, regardless of how it agrees with other cases’. It’s not even “the judgement of the people working on those taxa”, as the last and only decent study (McIntosh and Carpenter, 1998) concluded D. longus and D. cargegeii are distinct. Have you evaluated their reasons vs. Tschopp et al.’s? Did Tschopp et al. even use their characters?

Another problem is that enough of these kinds of cases will establish unofficial precedent regarding the way to handle less complete type specimens. I don’t care in particular about longus, but the result of your philosophy is that any more complete specimen is destined to become the type species or neotype. Thus we have a future where the principle of priority is meaningless, and don’t even try referring a more complete species to a known genus.

I’d like to add my thanks for the great discussion. I’m somewhat surprised at the continued attachment to the name “Brontosaurus,” as I suspected by now that most of us old brontophiles were going the way of the… dinosaurs. One of the ironies of the “return” of Brontosaurus is that the oldest and most famous mount over the years, AMNH 460, is an indeterminate apatosaurine (pending further study).

And ditto, it would be wonderful if the type specimens of ajax and excelsus at the Peabody were exhumed from the plaster and paint and studied thoroughly!

Several years ago, Virginia Tidwell taught a course in prep lab methods at the Denver Museum of Nature and Science, and we were permitted to (carefully!) step over the railings and put our eyeballs right up to the mounted dinosaur bones, to distinguish the restored casts from the unpainted bones. Would that all mounted bones were as accessible!

In response to my last post, about Horner’s quote” too many species have been named.” There is quite a bit of evidence to suggest ontogenetic variation is present among genera that were once thought to be different species. Dracorex it seems is now accepted as a juvenile Pachycephalosaurus(Horner and Goodwin 2009).
Another case can be made for the Triceratops and Torosaurus(Scannella and Horner 2010). (Longrich and Field 2012) added to the debate by presenting evidence that Torosaurus may still be valid. So although it is possible Torosaurus could be a full grown Triceratops, the debate is still on. Other species of ceratopsians could very well turn out to be juvenile forms of others (Brachyceratops and Avaceratops) just to name a few.
Carr has shown Nanotyrannus maybe a juvenile T-rex. Although Larson and Bakker still favor it as a separate genus. Again, it looks like a majority still think Nano is a juvenile rex. The findings show a reduced number of genera than was previously thought in the Hell Creek Formation. This ground breaking study should be applied to a number of dinosaurs in other formations.
I would not be surprised if Suchomimus turned out to be a subspecies of Baryonyx. Again more studies could possibly verify this. It seems more ontogenetic studies have been done on cretaceous dinosaurs than Jurassic ones.
As far as Morrison Formation sauropods are concerned, I think the only growth studies have been done by(Curry Rodgers 1999) and (Ikejiri 2005). I’m sure the sauropod experts on here know Curry-Rodgers’s study dealt with bone histology. While Ikejiri’s delt with the general ontogeny of Camarasaurus. (Foster 2005) pointed out that although the Morrison has samples of juveniles, adults seem to outnumber juveniles. Could adults outnumbering juveniles have to do with either environmental or preservation bias? A curious question raised overall about the dinosaur fossil record is, are most samples of full grown adults or sub-adults?
Also going back to the validity of Brontosaurus. Carpenter raised a good point in his post that he is concerned about all sauropod specimens becoming separate taxa. I agree with others on here that new preparation needs to be done on the various specimens of Apatosaurus and possibly other diplodocids in order to answer that question. Overall, it looks like Tschopp etl’s. new research could possibly start an Apatosaurine renaissance.

JR Foster, ” New Juvenile Sauropod Material in the Morrison Formation of Western Colorado and The Record of Record of Juvenile Sauropods from the Upper Jurassic Morrison Formation”: In Tidwell and Carpenter ‘s “Thunder-Lizards the Sauropodmorph Dinosaurs” 2005 Indiana University Press

Ikejiri, Tidwell, and Trexler,,” New Adult Specimens of Camarasaurus Lentus Highlight Ontogenetic Variation within the Species” in Tidwell and Carpenter’s “Thuder-Lizards the Sauropodmorph Dinosaurs” 2005 Indiana University Press

That is one thing that kinda puzzles me… How random the sperations at lot taxonomical levels (genera, species, subspecies) can be…

For example all extant monitor lizards are classified as members of the Varanus genus in spite of the fact that they vary wildly in size and some anaotmical features (like the shape and the number of cervical vertabra). I guess with long extinct species it becames even tougher…

Mickey: I’ve said all I have to say on this, and I suspect you have, too. My position: you can’t do good taxonomy without taste and judgement. Your position: we should be able to make a mechanistic algorithm that will give us an objectively correct taxonomy. Let’s come back in ten years and see whether the passage of time lends your position more weight.

Tom Johnson: yes, I am surprised how under-reported this paper’s finding on the AMNH apatosaur has been. To my mind, it’s the third headline, along with the return of Brontosaurus and the creation of Galeamopus. For those following along at home, Tschopp et al. found AMNH 460 outside their (Apatosaurus + Brontosaurus) clade, which on the face of it means that this specimen represents another new, as-yet-unrecognised, apatosaur. But of course future studies might well move it down within one of the two existing genera.

Matt (not Wedel): yes, we’ve very aware of the Horner Lab’s quest to synonymise all dinosaurs into ontogenomorphs of Triceratops. Like most palaeontologists, we appreciate their raising the important possibility of ontogenetic synonyms, but without buying into all their specific conclusions. For example, Matt and I wrote a detailed paper (some would say too detailed, and I wouldn’t necessarily disagree) refuting Woodruff and Fowler’s proposal that much Morrison-formation sauropod diversity could be explained by ontogenetic changes, particularly in neural-spine bifurcation. Similarly, our occasional collaborator Andy Farke, who is a ceratopsian jockey, is not persuaded by the Toroceratops hypothesis. We at SV-POW! don’t know enough about tyrannosaurs, spinosaurs or pachycephalosaurs to have informed opinions on the ontogenetic synonym proposals in those clades, but I will remind you of my question to Horner about this at the 2007 or 2008 SVP, and his response to it.

Hunter1324: yes, we’ve often noted here how inconsistently the ideas of “species”, “genus”, “family”, etc. are used across the tree of life — see for example my remark on Quercus in an earlier comment on this post. There is nothing to be done about this: the only conclusion to be drawn really is that these terms — the Linnean ranks — are meaningless.

Mossbrucker’s talk is on the Day 3 link and is the last interview of the day. Bakker is on there, too, but Mossbrucker’s discussion of the Apatosaur/Brontosaur skull they are removing from a sandstone block is the good stuff.

Honestly, I’m just a dino enthusiast and don’t pretend to have any advanced knowledge so would be interested what the experts make of it. (What kills me is that I actually visited to the Morrison museum a couple of weeks before I heard about “Kevin” and so didn’t make a point to ask about it. D’oh. Great little museum, though.)

“Diplodocus lacustris, YPM 1922*. The original type material of D. lacustris comprises
teeth, a premaxilla, and a maxilla (Marsh, 1884). However, personal observations at YPM
reveal that the cranial bones clearly belong to Camarasaurus or a morphologically similar
taxon, and that there is no relationship between them and the teeth. Mossbrucker & Bakker
(2013) described a newly found putative apatosaur maxilla and two premaxillae from the
same quarry, proposing that they might belong to the same individual as the teeth of YPM
1922. However, given the lacking field notes from the first excavations, such a referral
will be difficult to prove. Therefore, in the present analysis, only the teeth were scored for
D. lacustris.”

I was interested to see that botanists use the concept of ‘Section’ in order to organize clusters of species within genera (basically a ‘subgenus’). So for oaks (Quercus), there’s Sect. Quercus Sect. Mesobalanus, Sect. Cerrus, etc.

I know a lot of people complain about dinosaur workers being splitters, but how is this any different? Functionally, this is just shifting the ‘genus’ name into the section category. To me, highly speciose clades (like Quercus, Varanus, etc.) become harder to discuss in terms of evolutionary trends and relationships, because you don’t have convenient names to refer to clades within that genus.

I agree that part of the problem is having a binomial – if we just used one word to refer to a species (rather than the genus+species combo), then probably much disagreement would be avoided.

Victoria – There are ranks between genus and species in zoology too: subgenus, species group, species complex, superspecies, etc. They’re just not used much with dinos, which tend to have monospecific or paucispecific genera.

I know, that’s kind of my point – if non-dinosaur people are going to use subgenus, species complex, subspecies, etc., then I’m not sure why dinosaur workers are so often criticized for being splitters. We’re ultimately all dividing things up in the same way, we’re just using different names for the ‘ranks’ at which we do so.

I have avoided jumping into the discussion over nomenclatural rules in part because I’ve been trying to decide what I think. I came in with two long-held ideas: first, that names are hypotheses, and I tend not to get very wound up when they change because, hey, that’s what happens to hypotheses. And second, that nomenclatural practice is what taxonomists actually do, not just what the rules say they should do. I’m not saying that’s how things should be or would be in an ideal world, just that that’s how they are in our world, and any discussion of nomenclature that fails to acknowledge that is at odds with reality.

The new idea that I’ve had (new to me, anyway) is that nomenclatural rules are themselves hypotheses, and that may explain the disjunct between Mickey’s and Mike’s positions – and, not incidentally, why taxonomic practice frequently deviates from the rules as written. Or, more accurately, the ICZN guidelines are for some workers rules to be followed, and for other workers hypotheses to be adopted, modified, or rejected on a case-by-case basis. (Again, I’m not saying that’s how things should be, I’m saying that’s how they are. I don’t know how things should be – I am too peripherally involved in taxonomy to have given it enough thought.)

Furthermore, peoples’ attitudes toward the sanctity of the rules and existing names change over time and from place to place. A hundred years ago people tended to be more respectful of both. Now we are certainly more cavalier about sinking other people’s taxa and arguably more cavalier about following the rules as written. But in another century the pendulum may have swung back, or off in some new direction, or biological nomenclature may be grounded completely differently.

In part because I know those historical shifts are going to happen anyway, I tend to come down on the side of current utility. Should Tschopp et al. have resurrected Brontosaurus, or sunk Dinheirosaurus? Beats me. Let’s give it a few years and see if those decisions make it easier or harder to understand what’s going on with diplodocid diversity. They at least tried to come up with objective criteria for deciding what’s a species and what’s a genus, and I think that is a legitimate advance.

Cope had some interesting ideas on how genus distinctions should be made – mainly based on heterochrony, iirc. I’m not aware of anyone more recent who has a better criterion than “different enough” to justify genus-level distinctions.

Also, the specimen “Kevin” is mentioned in Tschopp et al. under the entry for Diplodocus lacustris.

Oops, sorry. Didn’t realize my earlier comment went through. Anyways, I tend to agree with Dr. Wedel, for what it’s worth. I’m more up on amphibian and fish taxonomy than dinosaur; it’s a whole different world when you have genera with hundreds of species. Are there any dinosaur genera with even ten species? Maybe Mamenchisaurus?

Thank you for the reply Mike. Although I think Horner and his group have made a great contribution to the study of ontogeny in dinosaurs. I must say your question to Horner really caught my attention. Although Draco could possibly be a juvenile Pachycephalosaur. His next proposal of Stygimoloch being the sub-adult seems to indeed run into problems, when you look at the horns of the base of the skull. No, modern day animal reabsorbs horn material. The tiny bony projections on the frills of triceratops though seem to be absorbed into the bone as it grows older. Those structures are probably different than pachy horns. Although I can’t say how different. Andy Farke should know.
Thanks also for the link of the paper that you and Matt Wedel wrote. I will most certainly read it, it looks like it great food for thought!
On an end note, seeing Brontosaurus possibly being valid again, is a great example of scientific progress. Careful evaluation of old finds can lead to some surprising new findings. In paleontology data can be valid for a while, until someone else finds new evidence making us look at things a different in way. That is the great thing about this new research on the diplodocids. Who knows what new research will present in a year to 10 years from now on the position of Brontosaurus.

‘Kevin’ is from Lakes Quarry 5 at Morrison which is from the lower part of Dinosaur zone 3; the holotype of A. ajax is from Lakes Quarry 10 which is much higher up in the uppermost Dinosaur zone 3.
So they probably aren’t the same species; Quarry 5 is closer in level stratigraphically to the Sheep Creek B. parvus and the Riggs Quarry 15 Diplodocidae indet. FMNH P 25112.

Well I suppose that’s the end of the “exchange”. I gotta tell you though, you came off as very David Peters-esque in these comments. Over at Pterosaur Heresies I’m used to presenting precise questions and having David simply ignore them in favor of some platitude, but I didn’t expect that here. That’s not utilizing “taste and judgement”, it’s holding a position for reasons entirely divorced from the data.

Let me restate what Mike said in that Tschopp et. al. got different results because they:

1) used more specimens and taxa
2) used a VERY radical method (specimen based phylogenic analysis)

The reason that their analysis seems so out there compared to the data we have already collected is because it uses a different system. As many have stated before, the scientific names given to the specimens in this paper are valid until proven otherwise. Until someone sees something wrong with their results and publishes a counter-paper on the subject, like it or not, Tschopp. et al.’s paper is valid. The issue with paleontological phylogeny is that we simply don’t have enough information to make, for the most part, accurate analyses. All the phylogenic information we collect is based on the Morphology of the specimen(s), Stratocladistical analysis and a handful of other methods. Until we find good samples of Diplodocoid DNA (which will most likely NEVER happen), the best we can do is make (highly) educated suppositions.

Well, Mickey, I can only assume you’re trying to provoke me with that analogy. It won’t work, because it’s evident nonsense.

What’s going on here is that you’re insisting that we both (A) need and (B) can have rigorous objective rules for when a type specimen or species needs to be changed. We can legitimately have different opinions about (A), but (B) is simply fantasy. There is and can be no system that does what you want.

If you think there is, then let’s see your concrete proposal.

Chase: doing your diplodocoid phylogenetic analysis at the specimen level is not that radical: Upchurch et al. (2005) did precisely this for Apatosaurus. In terms of recovering the phylogeny, I would characterise the Tschopp et al. paper as an incremental improvement (albeit a big increment) by including many more specimens and many more characters. In methodological terms, their innovations are in the attempt to formulate a quantitative rationale for lumping or splitting.

In one area, I disagree with you: you write “names are hypotheses”. Fundamentally, no: names are labels. They exist to allow us to unambiguously indicate specific things. It’s not a hypothesis that you’re Matt Wedel. It’s a fact. It won’t be overturned, because it’s more like an axiom than a conclusion. The name “Matt Wedel” exists in order to indicate you.

As I say, fundamentally names are not hypotheses. They great mistake of the Linnean binomial system is that, without meaning to, it makes names into hypotheses. Specifically, a binomial name such as Drosophila melanogaster is not just a label, but also encodes the phylogenetic hypothesis that the species melanogaster belongs to the genus Drosophila. In other words, it’s not actually a name at all, it’s an address. That’s why when the hypothesis changes (in this case, when melanogaster turns out to be more closely related to the type species of Sophophora than to that of Drosophila), the address of the species changes, and as a result of Linneus’s bonehead system, so does the name.

The solution — the obvious, obvious solution — is to use uninomials — names that are just names and not addresses. And this is precisely the solution that we are converging on in dinosaur palaeontology, where monospecific genera allow us to use the genus name alone as the identifier, with the species name being mere decoration (“proteles“, “proneneukos“) or an opportunity to honour a respected person (“macintoshi“).

The other way to get uninomials is to do what they’ve done in the monitor-lizard world: shove a whole gigantic clade into a single genus Varanus, and use the species name as an effective uninomial. That’s OK for deeply nested species that are definitely part of the clade, but it doesn’t solve the problem for species near the origin of the clade that might be in and out, and which may or may not therefore have the presumed address (is it Varanus priscus or Megalania priscus?).

Bottom line: the way dinosaur workers are doing this is objectively superior.

(I can see that for clades with many, many species, it’s convenient as a simple matter of generating enough names to use a Genus × species cross-product — then you only have to think up sqrt(n) times as many unique names. But it’s bad nomenclatural practice.)

Names are only labels for holotypes. For every other specimen – which is most of them – the name is a hypothesis about relatedness. That will still be true even if your Shiny Uninomial Future comes to pass.

Also, just slapping uninomials on things does not answer the question, “Is this new specimen nameably distinct from all of the previously known specimens?” Unless you are proposing that every single specimen get a uninomial identifier. I doubt that’s what you mean, but I could be wrong – feel free to clarify.

Names are only labels for holotypes. For every other specimen – which is most of them – the name is a hypothesis about relatedness.

That is a very important observation, and one that I’ve never seen spelled out before.

In fact, three different kinds of thing (at least) can all bear the same name: 1, a holotype; 2, a referred specimen; and 3, the concept of the species. All of these things can be called Brachiosaurus brancai“, but it means something different in each case. For #1, it’s a label which should be all rational criteria be immutable. For #2 it is, as you right say, a hypothesis. And for #3 it’s … I hardly know what to call it. A speculation?

Switching to uninomials fixes the problem with #1 — it makes labels immutable. As you rightly point out, it does nothing for #2 (nor, for that matter, for #3). I don’t think that’s a drawback, though. The fact that #2 and #3 are a hypothesis and a speculation is not a problem with them, it’s just what they are.

[…] the results in your paper so that a wider audience can understand them. You can find those posts here and here. Dave Hone talks about his paper on combat and cannibalism among tyrannosaurs (see […]

Hunter1324, do you know of a reference for that cervical variation in Varanus? Back when I was doing my PhD I was sure I’d read it in Hoffstetter & Gasc (I think) but was never able to track down where the statement was published. It’s kind of slipped my mind for most of the last two decades (there are some fossil cervical vertebrae on my back burner for which a citation would be highly relevant).

We at SV-POW! don’t know enough about tyrannosaurs, spinosaurs or pachycephalosaurs to have informed opinions on the ontogenetic synonym proposals in those clades, but I will remind you of my question to Horner about this at the 2007 or 2008 SVP, and his response to it.

To be fair, they’ve since done histology on those skulls. “Stygimoloch” really was actively resorbing its spikes, bizarre though that is.

I was interested to see that botanists use the concept of ‘Section’ in order to organize clusters of species within genera (basically a ‘subgenus’).

The ICZN has fixed the number of genus-group and species-group ranks: genus, subgenus, “group of species”, species, “group of subspecies”, subspecies. That’s it, no further ranks are allowed between or below these. Taxa at only two levels are allowed to be named between Varanus and its species. If you want to talk about more than those, you are forced to split the genus. That’s why zoologists are splitters compared to botanists when it comes to genera.

(I’ve never seen a “group of subspecies” used. “Species groups” or “superspecies”, however, were common in such large genera as Rana and Bufo before the great splittings of 2006.)

As many have stated before, the scientific names given to the specimens in this paper are valid until proven otherwise. Until someone sees something wrong with their results and publishes a counter-paper on the subject, like it or not, Tschopp. et al.’s paper is valid.

Have you read the rest of this thread? Names aren’t something that can be proven invalid by a phylogenetic analysis; nomenclature isn’t science, it’s a set of arbitrary conventions, and Tschopp et al. don’t pretend otherwise – they merely propose to make some of our conventions internally consistent.

[…] and big back end, this is clearly a diplodocid. The neck is too skinny for Apatosaurus or the newly-resurrected Brontosaurus, and too long for Diplodocus. I lean toward Barosaurus, although I noticed in going back through […]

[…] to tell broken vertebrae of Camarasaurus from those of Apatosaurus (at the time; Brontosaurus is back in contention now). Here’s a thing I made up to help me sort out cervical centra of Camarasaurus and whatever […]

Oof: I’ve learned from past comments I’ve made, that I should read the comments that appear below this spot before returning… oof, fascinating.

But no one asked my out of the box non-expert question: the 2nd to last picture of AMNH 460, why are the legs splayed so much? The femoral side of the knee joint is clearly misaligned to the properly-vertical lower limb. I mean, if you look at a cow from the back, or a train car, the feet seem improbably close together for something so obviously topheavy. That was supposedly a major “dinosaurian” character, vertical legs….

At the danger of reopening a 3 year old flame war, I have to think that Linnaeus was trying to do something quite different than Darwin. I assume Linnaeus was trying to categorize biodiversity into what he thought were G-d given categories and supercategories, which seems at least reasonable if you assume species are immutable and directly created by G-d, that there’d be some hierarchy and order.

Given our basic modern understanding of some tree of life, those categories aren’t a priori present – and I suspect that’s why Mike calls them meaningless – they’re simply convenient ways of a posteriori trying to tease out actual tree-of-life relationships, sort of like using directories and subdirectories in a computer file management system, where you can keep adding more layers as convenient when any particular grouping of files gets too large to be useful to a human user. This would be …someone, sorry, this was already 2 hours I wasn’t planning to spend… someone’s name-as-hypothesis.

I mean, If there were only 10 extant species, Linnaeus wouldn’t have bothered. Or there’d only be 3 levels….

But there is a definition of “species” that I thought was factual: a group of individuals that can interbreed. Is that still used? The only problem with that that I can immediately think of is of 3 sister groups recently diverged, where A can interbreed with B, and B with C, but not A and C…

The interbreeding criterion for species has lots of holes. To pick a couple of examples from opposite ends of the spectrum:
– In some big old redwoods and sequoias, there has been so much genetic divergence on different branches over the centuries and millennia that pollen from one branch can sometimes fail to fertilize cones on a different branch. So by the interbreeding criterion, there has been a speciation event within a single individual tree.
– Some species can interbreed successfully even though in the wild they tend to maintain morphologically and behaviorally distinct groups. South American ducks come to mind – they hybridize so freely that if interbreeding is the species criterion, there aren’t ducks, there’s just duck.

In any case, there are lots of species concepts that are factual, it just depends on which facts we think are important. There is a long and deep literature here that I am not going to try to summarize. But if you want an interesting perspective on species concepts, try de Queiroz (1998) on the general lineage concept of species, which is a free download here. I’m sure the literature has moved on in the past 20 years – I read that paper waaaay back in grad school – but the review of other species concepts will at least give you an idea of how much thought and effort has gone into this.

Brad, the AMNH apatosaur mount’s hindlimbs are not particularly splayed, they are merely posed mid-stride and this image is from an angle whether they appear to diverge. See the photo of the same specimen in this followup post.

On what “species” means, I’ve yet to see a more truthful definition than the I saw attributed to John Ostrom: “It’s pretty much whatever a good taxonomist says it is”.